Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling DOI Creative Commons
Marcus B. Smolka,

Will Comstock,

M.V.A.S. Navarro

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information is crucial deconvolute complex signaling networks, interrogate multifaceted actions, and assess drug effects or genetic perturbations. Here we developed a proteomic sensor platform (ProKAS) for analysis using mass spectrometry. ProKAS based on tandem array peptide sensors with amino acid barcodes that allow multiplexed spatial, kinetic, screening applications. We engineered module simultaneously monitor activities DNA damage response kinases ATR, ATM, CHK1 genotoxic drugs, while also uncovering differences between these responses nucleus, cytosol, replication factories. Furthermore, an silico approach rational design specific substrate peptides expandable other kinases. Overall, novel versatile system systematically spatially probing cells.

Language: Английский

Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023 DOI Creative Commons
Ronghui Lou, Wenqing Shui

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(2), P. 100712 - 100712

Published: Jan. 4, 2024

Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate and reproducible quantitative proteomics. This review provides comprehensive overview of recent advances in both the experimental computational methods DIA proteomics, from data schemes to analysis strategies software tools. are categorized based on design precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, parallel accumulation-serial fragmentation (PASEF)-enhanced methods. For analysis, major classified into spectrum reconstruction, sequence-based search, library-based de novo sequencing sequencing-independent approaches. A wide array tools implementing these reviewed, with details their overall workflows scoring approaches at different steps. The generation optimization spectral libraries, which critical resources also discussed. Publicly available benchmark datasets covering global proteomics phosphoproteomics summarized facilitate performance evaluation various workflows. Continued synergistic developments versatile components expected further enhance power DIA-based

Language: Английский

Citations

45
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry DOI Creative Commons
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster

et al.

ACS Measurement Science Au, Journal Year: 2024, Volume and Issue: 4(4), P. 338 - 417

Published: June 4, 2024

Proteomics is the large scale study of protein structure and function from biological systems through identification quantification."Shotgun proteomics" or "bottom-up prevailing strategy, in which proteins are hydrolyzed into peptides that analyzed by mass spectrometry.Proteomics studies can be applied to diverse ranging simple proteoforms, protein-protein interactions, structural alterations, absolute relative quantification, post-translational modifications, stability.To enable this range different experiments, there strategies for proteome analysis.The nuances how proteomic workflows differ may challenging understand new practitioners.Here, we provide a comprehensive overview proteomics methods.We cover biochemistry basics extraction interpretation orthogonal validation.We expect Review will serve as handbook researchers who field bottom-up proteomics.

Language: Английский

Citations

30
The solute carrier superfamily interactome DOI Creative Commons
Fabian Frommelt, René Ladurner, Ulrich Goldmann

et al.

Molecular Systems Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 12, 2025

Abstract Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of diverse substrates including nutrients, ions and drugs. There are about 450 different SLCs, residing in variety subcellular membranes. Loss-of-function an unusually high proportion SLC is genetically associated with plethora human diseases, making SLCs rapidly emerging but challenging drug target class. Knowledge their environment may elucidate the molecular basis for functional integration metabolic cellular pathways help conceive pharmacological interventions based on modulating proteostatic regulation. We aimed at obtaining global survey SLC-protein interaction landscape mapped protein–protein interactions 396 by proteomics. employed assessment RNA interference interactors combination measurement stability localization. As example, we detail role SLC16A6 phospho-degron contributions PDZ-domain proteins LIN7C MPP1 to trafficking SLC43A2. Overall, our work offers resource scientific community.

Language: Английский

Citations

4
XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis DOI Creative Commons
Ying‐Lan Chen, Fan-Wei Lin,

Kai-Tan Cheng

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 4, 2023

Abstract Proteolytic activation of cytokines regulates immunity in diverse organisms. In animals, cysteine-dependent aspartate-specific proteases (caspases) play central roles cytokine maturation. Although the proteolytic production peptide is also essential for plant immunity, evidence regulating still limited. this study, we found that C-terminal processing a caspase-like substrate motif “CNYD” within Pathogenesis-related protein 1 (PR1) generates an immunomodulatory (CAPE9) Arabidopsis . Salicylic acid enhances CNYD-targeted protease activity and release CAPE9 from PR1 This process involves exhibiting enzyme activity, identified as Xylem cysteine peptidase (XCP1). XCP1 exhibits calcium-modulated pH-activity profile comparable to human caspases. required induce systemic triggered by pathogen-associated molecular patterns. work reveals key which produces canonical salicylic signaling marker activate immunity.

Language: Английский

Citations

28
The 2023 Report on the Proteome from the HUPO Human Proteome Project DOI
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(2), P. 532 - 549

Published: Jan. 17, 2024

Since 2010, the Human Proteome Project (HPP), flagship initiative of Organization (HUPO), has pursued two goals: (1) to credibly identify protein parts list and (2) make proteomics an integral part multiomics studies human health disease. The HPP relies on international collaboration, data sharing, standardized reanalysis MS sets by PeptideAtlas MassIVE-KB using Guidelines for quality assurance, integration curation non-MS neXtProt, plus extensive use antibody profiling carried out Protein Atlas. According neXtProt release 2023-04-18, expression now been detected (PE1) 18,397 19,778 predicted proteins coded in genome (93%). Of these PE1 proteins, 17,453 were with mass spectrometry (MS) accordance 944 a variety methods. number PE2, PE3, PE4 missing stands at 1381. Achieving unambiguous identification 93% encoded from across all chromosomes represents remarkable experimental progress list. Meanwhile, there are several categories that have proved resistant detection regardless protein-based methods used. Additionally some PE1–4 probably should be reclassified PE5, specifically 21 LINC entries ∼30 HERV entries; being addressed present year. Applying wide array biological clinical ensures other omics platforms as reported Biology Disease-driven teams pathology resource pillars. Current positioned transition its Grand Challenge focused determining primary function(s) every itself networks pathways within context

Language: Английский

Citations

16
Pervasive mislocalization of pathogenic coding variants underlying human disorders DOI
Jessica Lacoste,

Marzieh Haghighi,

Shahan Haider

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(23), P. 6725 - 6741.e13

Published: Sept. 30, 2024

Language: Английский

Citations

13
Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein DOI
Cherrelle Dacon,

Re’em Moskovitz,

Kristian E. Swearingen

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6729)

Published: Jan. 2, 2025

The most advanced monoclonal antibodies (mAbs) and vaccines against malaria target the central repeat region or closely related sequences within Plasmodium falciparum circumsporozoite protein (PfCSP). Here, using an antigen-agnostic strategy to investigate human antibody responses whole sporozoites, we identified a class of mAbs that cryptic PfCSP epitope is only exposed after cleavage subsequent pyroglutamylation (pGlu) newly formed N terminus. This pGlu-CSP not targeted by current anti-PfCSP included in licensed vaccines. MAD21-101, potent mAb this class, confers sterile protection Pf infection liver–chimeric mouse model. These findings reveal site vulnerability on sporozoite surface can be next-generation antimalarial interventions.

Language: Английский

Citations

2
Widespread release of translational repression across Plasmodium’s host-to-vector transmission event DOI Creative Commons
Kelly T. Rios, James P. McGee, Aswathy Sebastian

et al.

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(1), P. e1012823 - e1012823

Published: Jan. 8, 2025

Malaria parasites must respond quickly to environmental changes, including during their transmission between mammalian and mosquito hosts. Therefore, female gametocytes proactively produce translationally repress mRNAs that encode essential proteins the zygote requires establish a new infection. While release of translational repression individual has been documented, details global have not. Moreover, changes in spatial arrangement composition DOZI/CITH/ALBA complex contribute control are also not known. we conducted first quantitative, comparative transcriptomics DIA-MS proteomics Plasmodium across host-to-vector event document repression. Using zygotes P . yoelii , found ~200 transcripts released for translation soon after fertilization, those encoding functions. identified many remain repressed beyond this point. TurboID-based proximity regulatory revealed substantial and/or compositional event, which consistent with recent, paradigm-shifting models control. Together, these data provide model mechanisms promote Plasmodium’s efficient from host vector.

Language: Английский

Citations

2
A eukaryotic-like ubiquitination system in bacterial antiviral defence DOI
Lydia R. Chambers, Qiaozhen Ye, Jiaxi Cai

et al.

Nature, Journal Year: 2024, Volume and Issue: 631(8022), P. 843 - 849

Published: July 17, 2024

Language: Английский

Citations

9
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins DOI Creative Commons
Eric W. Deutsch, Leron W. Kok, Jonathan M. Mudge

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 9, 2024

A major scientific drive is to characterize the protein-coding genome as it provides primary basis for study of human health. But fundamental question remains: what has been missed in prior genomic analyses? Over past decade, translation non-canonical open reading frames (ncORFs) observed across cell types and disease states, with implications proteomics, genomics, clinical science. However, impact ncORFs limited by absence a large-scale understanding their contribution proteome. Here, we report collaborative efforts stakeholders immunopeptidomics, Ribo-seq ORF discovery, gene annotation, produce consensus landscape protein-level evidence ncORFs. We show that at least 25% set 7,264 give rise translated products, yielding over 3,000 peptides pan-proteome analysis encompassing 3.8 billion mass spectra from 95,520 experiments. With these data, developed an annotation framework created public tools researchers through GENCODE PeptideAtlas. This work will provide platform advance ncORF-derived proteins biomedical discovery and, beyond humans, diverse animals plants where are similarly observed.

Language: Английский

Citations

8